3M3D | pdb_00003m3d

Crystal structure of Acetylcholinesterase in complex with Xenon

• PDB DOI: https://doi.org/10.2210/pdb3M3D/pdb

• Classification: HYDROLASE
• Organism(s): Tetronarce californica
• Mutation(s): No 


• Deposited: 2010-03-09 Released: 2011-03-09 
• Deposition Author(s): Behnen, J., Brumshtein, B., Toker, L., Silman, I., Sussman, J.L., Klebe, G., Heine, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.200 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.187 (DCC) 

Literature

Old acquantance rediscover; use of xenon/protein complexes as a generic tool for SAD phasing of inhouse data

Behnen, J., Krueger, H., Brumshtein, B., Toker, L., Silman, I., Sussman, J.L., Klebe, G., Heine, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.86 kDa 
• Atom Count: 4,505 
• Modeled Residue Count: 532 
• Deposited Residue Count: 543 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A	543	Tetronarce californica	Mutation(s): 0  EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica) Explore P04058  Go to UniProtKB:  P04058
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
XE	B [auth A], C [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
PEG	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.200 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.187 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.769	α = 90
b = 111.769	β = 90
c = 137.232	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
HKL2Map	model building
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Behnen, J., Brumshtein, B., Toker, L., Silman, I., Sussman, J.L., Klebe, G., Heine, A.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-11-27
  Changes: Data collection, Database references, Structure summary